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This is something i have always been interested in as well. I found a good article on it today that you guys might be interested in:
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Some physicians condemn squats citing how destructive they are to the knees despite scientific studies and millions of personal experiences to the contrary. One sports medicine doctor explained to me why squats were considered to be bad for the knee. He was actually telling me this between his sets of squats! Since sports medicine doctors only see people with injuries, one can guess why they may have developed this belief. The individuals they treat certainly do not a constitute a random sample, let alone a representative population, as any scientist knows is essential to even attempt to formulate inferences.

The NSCA position statement notes:

"Some reports of high injury rate may be based on biased samples. Others have attributed injuries to weight training, including the squat, which could have been caused by other factors. Injuries attributed to the squat may result not from the exercise itself, but from improper technique, pre-existing structural abnormalities, other physical activities, fatigue or excessive training."

An early study suggested deep knee bends with weights (squats) were hazardous to the ligamentuous structures of the knee. Later studies conclude squats improve knee stability if the lifting technique does not place rotary stresses on the knee (Fleck and Falkel, 1986). The NSCA state:

"Squats, when performed correctly and with appropriate supervision, are not only safe, but may be a significant deterrent to knee injuries."

Torque Force
Contrary to propaganda to the contrary, prominent weight training authorities demonstrate the squat with the knees flexing forward at the same distance as the hips flex backwards. Fredrick Hatfield, Ph.D., the first man to squat over 800 lbs, recommends the knees to extend over the feet with the back more upright for quadriceps development. "Strength Training for Young Athletes" by Steven J. Fleck, PhD and William J. Kraemer, PhD, illustrate parallel squats with the knees extending beyond the feet (knees moving forward with same magnitude as hip moving backwards).

Torque force is necessary for the muscles and joint structures to adapt to the respected overload. If the knee does not travel forward during the barbell squat, the quadriceps muscles are not significantly exercised. On the other hand, injury may result if the knee or lower back experience greater torque forces than what they are accustom.

Fry et. al. (2003) examined the hip and knee torque forces of variations of parallel barbels squats and concluded appropriate joint loading during this exercise may require the knees to move slightly past the toes.

Try this simplified qualitative method in determining relative torque forces in the knee and hip joints. First take a photograph of the barbell squat in a full decent with a perspective perpendicular to the joints plane. Draw a line of force through the resistance on its center of gravity, straight up and down, parallel to the force of gravity. Gravity acting on both the body mass and added mass (barbell) contribute to the resistance. On the barbell squat, the center of gravity is between the forefoot and heel. If it is not, the individual will fall over, toward the center of gravity. Incidentally, compression forces act upon the joints during the squat stance.

During the execution of a barbell squat, the knees and the hips travel in opposite directions away from the foot, or away from the center of gravity. Draw a second line on the knee joint parallel to the line of force. Draw a third line on the hip joint parallel to the previous lines. A relative comparison can be made on the torque forces of the knee and hip. Typically the torque forces are similar for the knee and hip joints on the barbell squat; the knees travel forward the same magnitude as the hips travel backwards. Generally speaking, during a powerlift type squat (bar lower behind the shoulders and a wider stance) the knee does not travel forward as far as a bodybuilding type squat. The hips typically travel back further with the torso bent forward on a powerlift type squat. This emphasizes the stronger hip extensors and consequently reduces knee extensor involvement. Knee torque is further reduced by a wide stance.

Rotary Force
The practice of adopting foot rotation to selectively strengthen individual muscles of the quadriceps is not supported by the literature (Boyden 2000; Signorile 1995). Knee rotation during the squat can increase the risk of injury (Fleck and Falkel, 1986). Signorile, et. al. states:

"Extreme outward toe point greatly reduces stability, it does not allow the proper drift of the hips as the lifter descends... Extreme inward toe points are equally dangerous, coupling the same problems of stability, base size and lower body drift with the added danger of bringing the knees together...this movement would place high stress on all connective tissue."

Full (Deep) Squat
Kreighbaum (1996) illustrate the safe position of a deep squat with the knees extending beyond the toes. Kreighbaum explains how a deep squat can be performed little chance of injury to the knee. The variables of concern:

speed of descent
size of calves and thighs
strength of the controlling muscles
The primary danger to the knee occurs when the tissues of the calf and thigh press together altering the center of rotation back to the contact area creating a dislocation effect. The danger of knee injury in this situation may be prevented if either of the following factor are present:

center of gravity of the body system is keep forward of the altered center of rotation
muscles of the thigh are strong enough to prevent the body from resting or bouncing on the calves.
Kreighbaum conclude the deep squat is of little danger to the knees unless these variables and factors are disregarded. Certainly only a limit type of athletes may have a sports specific need to perform a full squat. Olympic weightlifters commonly bounce out of a full front squat with near maximum resistances during both the Clean &amp; Jerk and Snatch. Incidentally, the wide stance during an Olympic style squat further reduces knee torque forces.

During the lower portions of the deep squat the lower back may flex if hip flexibility is inadequate. The risk of injury is increased if the muscles of the lower back are not strong enough to support the flexed spine or the joint structures have not progressively adapted to such a stress. Flexibility exercises can be performed if hip flexibility is insufficient for deep, or full squats. See Full Squat Flexibility.

Customization
If the body has not adapted to a greater torque force, injury can result. It is not necessary to avoid the torque force if the muscles and joint structures can adapt. See adaptation criteria. Of the hip and knee joint, the knee is more vulnerable to injury than the hip due to structural and functional differences. Certainly, if an individual has had a history of knee pain associated with these types of movements, the squat can be modified to to place more torque on the hip and consequently less on the knee joint. Based on the above analysis, this can be accomplished two ways. Simply by not squatting down all the way (e.g. 90į) both the knees and hip do not experience as great of torque forces. Although, this decrease is often off set by the tendency to add more weight to the exercise. Alternatively, by bending at the hip more than the knee, the knee will travel forward less, as in the powerlifting type squat. Recall, the quadriceps will not be exercises as intensely since there is less torque on the knee joint. In addition, since balance must be maintained over the feet, bending over not only transfers more torque to the hips, the torque forces through the spine (lower back) increase; another vulnerable joint for some. Certainly a compromise must be made to evenly distribute the torque force between the knee and the hip / lower back, particularly when both the knees and lower back are healthy.

If the ankle is not flexible enough to allow the knee to travel forward sufficiently, the back will need to be bent forward more to maintain the center of gravity within the foot base. Consequently the lower back with be subjected to greater torque forces. Squatting with the feet wide apart can alleviate part of the problem, allowing the back to be positioned more upright. This solution does not, however, distribute equal stresses on the quadriceps and glutes as would be possible with adequate ankle flexibility.

Until flexibility can be restored, a temporary solution is to elevate the ankles on a board or platform. This will allow the knees to travel forward the same distance as the hip travels backwards. Elevating the heels may present a risk to individuals with adequate ankle flexibility who have not adapted to greater torque forces through the knee. In which case, the knees can potentially travel forward more than what they are accustom. Even when elevating the heels with insufficient ankles flexibility, resistance should begin light and progress only 5-10% every workout until a true workout weight is achieved so joint adaption can occur.

Obviously, individuals who are at a higher risk for specific types of knee pain may choose to avoid certain exercises specifically designed to emphasis the quadriceps involvement by increased knee torque (e.g. front squats, sissy squats, safety squats, barbell hack squats, leg extensions). Likewise, individuals who are at a greater risk for particular types of lower back pain may choose to avoid certain exercises specifically designed to lower back involvement by increased lower back torque (e.g. squats, deadlifts) or hip torque (e.g. deep glute exercises).

I have been wondering for the longest time how to increase hip range of motion.... there is a picture on the exercise description of exrx.net... the man is performing full squats with incredible hip flexibility. How is that kind of range of motion achieved? I have been full squatting for years and still can't get my hips to flex that much... I don't know who to contact on this site, perhaps you can put me in contact with someone who knows the man in the picture or who has some insight into this?

Although it is possible for the spine to adapt to less than idea hip flexibility in healthy individuals, it is generally recommended that a full squat be performed with adequate hip flexibility to avoid the posterior pelvic rotation at the lowest position.

Flexibility may be limited by muscular, joint, or body segment girth constraints. An comprehensive qualitative assessment can be performed to determine an individualized flexibility program. Dynamic flexibility under a load, rather than static flexibility, will be more applicable to squat range of motion. This can be achieved by having an experienced squatter examine the subjects technique during a free hand squat with arms foward or a squat with a light weight.

Full squats may be appropriate for certain athletes who require strength and joint stability in these lower positions (like performing Olympic style weightlifts). A parallel squat may be sufficient to achieve many individual's conditioning goals. Keep in mind too great of flexibility may not necessarily be a favorable attribute for all sports (See Stretching and Flexibility).

Keep in mind full range will vary from person to person. For example, An individual with large calves and thighs may not even be able to achieve a parallel position since their calf and lower hamstring would be smashed together in this position. one should only perform full range for their particular range of motion. Even a three quarter squat may end up challenging some people's flexibility.

The soleus or ankle joint may be suspect if the heal can not be kept on the floor while the knee passes over the knee in the squat position. See doriflexion inflexibility.

When assessing the knee's range of motion during the squat, the relative position of the leg should be noted when the knee and lower hamstring are compressed together.

The flexibility of the hip joint can also assessed during the squat. As the subject performs the full squat, the point of when the pelvis turns under (posterior rotation) should be noted. The compression of abdomen against the upper thigh may be a limiting factor for some individuals.

If the pelvis posteriorly rotates prematurely, further assessment can be performed to determine if the flexibility of the gluteus maximus or the adductor magnus is deficient.

To assess the adductor magnus, the subject would lie supine on a mat. The assessor would slowly move the bent knee toward the subject's arm pit (on the same side). The angle of the hip when the pelvis begins to posteriorly rotates should be noted.

To assess the gluteus magnus, a similar test would be performed, except the hip would first be externally rotated so the bent knee points outward. Then the lower would be slowly moved toward the subject chest. Again the angle of the hip when the pelvis begins to posteriorly rotates should be noted.

Dynamic flexibility movements (i.e. deep squats with body weight or empty bar) can be performed immediately before squatting. Static stretching for the gluteus maximus and/or the adductor magnus (depending on assessment above) can be performed immediately following a weight training session.

Stretches for Adductor Magnus (see bottom)
Stretches for Gluteus Maximus
A wider stance often allows those with flexibility issues to squat deeper. Just remember to keep the knees orientated the same direction of the feet.

When introducing new form (i.e. fuller range of motion, wider stance, etc) allow for adaptation which includes adequate recovery and progressive loads over time. Also see Adaptation Criteria. For advanced trainees, periodization with varying workloads (i.e. light heavy days) may be required for adoption for continued progress.

"The truth Iíve discovered is that you donít have to lift enormous weights to grow muscle. By using stricter form, slower negatives, and stretching between sets you can get an incredible pump in all your workouts. Numbers are an abstraction, especially to muscles. Your body doesnít know the absolute weight of what you lift, it only recognizes how heavy it feels. The secret is to make lighter weights feel heavier. " - Frank Zane

"Sacrifice: To give up, destroy, renounce, and surrender your ego, excuses, bad habits, fears, and your couch - in the belief of an ideal or pursuit of a worthy goal."

Well, I discovered a lot of things, donít take them as being fully scientific though. Many people suggest doing leg extensions before sissy squats either as a warm-up (to protect your knees) or in a superset. I found that the contraction of the muscle is very different in the leg extension then in the sissy squat and can present problems to certain people. The peak contraction in the leg extension is at the top of the movement so one can assume that the quadriceps muscle will be shortened after a set of these just like a set of concentration curls will work the biceps peak. Therefore, a larger amount of stress is placed on the knee joint if one precedes sissy squats with leg extensions. This could cause all kinds of pain and popping in the knee joint that wouldnít occur if one did a different warm-up. It seems to work for me. Stretching before sissy squats probably helps as well but if your muscle is tense enough it might not be sufficient. I found that this was about the only way that I could do sissy squats. I look at it like this, when people donít grow they blame genetics, when people canít do some of these exercises they blame knee problems. Donít we know better than that? If you have a bad back arenít you supposed to reinforce it not avoid all exercises that involve the slightest amount of pressure on the back? Look at Arnold who learned to do seated cable rows with a full stretch, look at his Christmas tree. I was also wondering if any one knew anything about knee pressure, you know people who have to wrap their knees. What causes our knees to deteriorate like this? How can we improve the pressure in our knees? Thanks for the article Mac and all the references, it is useful information in my quest. I hope I have not forgotten anything, long post you know.